Using 500k for a single will make it brighter, maybe unwantedly so. Conversely, using 250k for the humbucker would make them darker sounding with less treble.
Think on Fender's humbucker equipped guitars they use 250k pots. Personally I'd try to get the best of both worlds, when i had my HSS strat i set it up with 2 volumes, a 500k for the humbucker and 250 for the singles. Might not work in your case, never tried a HSS setup.
Best bet is probably trying both combinations out. If i remember correctly the value of the tone control isn't as important as the volume's.